comprehensive-workflow-for-genome-wide-identification-expression-meta

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Classification and nomenclature of genes in a family can significantly contribute to the description of the diversity of encoded proteins and to the ...

Nitric oxide (NO) is a highly reactive molecule that rapidly diffuses and permeates cell membranes. In animals, NO is implicated in a number of diverse physiological processes, such as neurotransmission, vascular smooth muscle relaxation, and platelet inhibition. It may have beneficial effects, e.g., as a messenger in immune responses, but it is also potentially toxic when the antioxidant system is overwhelmed and reactive oxygen intermediates (ROI) accumulate. During the last few years, NO has been detected in several plant species, and an increasing number of reports on its function have implicated NO as an important effector in plant growth, development, and defense. The broad chemistry of NO involves an array of interrelated redox forms with different chemical reactivities and numerous potential biological targets in plants. NO signaling functions depend on its reactivity. ROI are key modulators of NO in triggering cell death, but the nature of the mechanisms by which this occurs in plants is different from those commonly observed in animals. This review focuses on the signaling functions of NO, when channeled through the cell death pathway by ROI.

The functions of nitric oxide-mediated signaling and changes in gene expression during the hypersensitive response.

The smaller isoform of the enzyme glutamic acid decarboxylase (GAD65) is a major islet autoantigen in autoimmune type 1 diabetes mellitus (T1DM). Transgenic plants expressing human GAD65 (hGAD65) are a potential means of direct oral administration of the islet autoantigen in order to induce tolerance and prevent clinical onset of disease. We have previously reported the successful generation of transgenic tobacco and carrot that express immunoreactive, full-length hGAD65. In the present study, we tested the hypothesis that the expression levels of recombinant hGAD65 in transgenic plants can be increased by targeting the enzyme to the plant cell cytosol and by mediating expression through the potato virus X (PVX) vector. By substituting the NH2-terminal region of hGAD65 with a homologous region of rat GAD67, a chimeric GAD67(1-87)/GAD65(88-585) molecule was expressed in transgenic tobacco plants. Immunolocalization analysis showed that immunoreactive GAD67/65 was found in the plant cell cytosol. By using a radio-immuno assay with human serum from a GAD65 autoantibody-positive T1DM patient, the highest expression level of the recombinant GAD67/65 protein was estimated to be 0.19% of the total soluble protein, compared to only 0.04% of wild-type hGAD65. Transient expression of wild-type, full-length hGAD65 in N. benthamiana mediated by PVX infection was associated with expression levels of immunoreactive protein as high as 2.2% of total soluble protein. This substantial improvement of the expression of hGAD65 in plants paves the way for immunoprevention studies of oral administration of GAD65-containing transgenic plant material in animal models of spontaneous autoimmune diabetes.

Improved in planta expression of the human islet autoantigen glutamic acid decarboxylase (GAD65).

Nitric oxide (NO) is an essential regulatory molecule in several developmental processes and in the stress response in both animal and plant systems. Furthermore, key features of plant resistance to pathogens have been shown to depend on NO production, e.g., defense gene expression and the activation of a hypersensitive reaction (HR) in synergy with reactive oxygen species (ROS). Due to the many possible mechanisms of NO action, a clear picture of its involvement in plant resistance to pathogens is far from being achieved. Transcriptional changes related to NO action are likely to play a significant role in resistance and cell death. We investigated the changes in the expression profiles of Arabidopsis thaliana following infiltration with the NO donor sodium nitroprusside, by cDNA-amplification fragment length polymorphism (AFLP) transcript profiling. Altered expression patterns were detected for 120 of the approximately 2,500 cDNAs examined. Sequence analysis revealed homologies with genes involved in signal transduction, disease resistance and stress response, photosynthesis, cellular transport, and basic metabolism or with sequences coding for unknown proteins. Comparison of the expression profiles with data from public microarray sources revealed that many of the identified genes modulated by NO were previously reported to be modulated in disease-related experiments.

Nitric oxide-mediated transcriptional changes in Arabidopsis thaliana.

Cross talk between reactive nitrogen and oxygen species during the hypersensitive disease resistance response.

Nitric oxide (NO) is involved in diverse physiological processes in plants, including growth, development, response to pathogens, and interactions with beneficial microorganisms. In this work, a dedicated microarray representing the widest database available of NO-related transcripts in plants has been produced with 999 genes identified by a cDNA amplified fragment length polymorphism analysis as modulated in Medicago truncatula roots treated with two NO donors. The microarray then was used to monitor the expression of NO-responsive genes in M. truncatula during the incompatible interaction with the foliar pathogen Colletotrichum trifolii race 1 and during the symbiotic interaction with Sinorhizobium meliloti 1,021. A wide modulation of NO-related genes has been detected during the hypersensitive reaction or during nodule formation and is discussed with special emphasis on the physiological relevance of these genes in the context of the two biotic interactions. This work clearly shows that NO-responsive genes behave differently depending on the plant organ and on the type of interaction, strengthening the need to consider regulatory networks, including different signaling molecules.

Expression of Medicago truncatula genes responsive to nitric oxide in pathogenic and symbiotic conditions.

In recent years a particular class of probabilistic graphical models-called topic models-has proven to represent an useful and interpretable tool for understanding and mining microarray data. In this context, such models have been almost only applied in the clustering scenario, whereas the classification task has been disregarded by researchers. In this paper, we thoroughly investigate the use of topic models for classification of microarray data, starting from ideas proposed in other fields (e.g., computer vision). A classification scheme is proposed, based on highly interpretable features extracted from topic models, resulting in a hybrid generative-discriminative approach; an extensive experimental evaluation, involving 10 different literature benchmarks, confirms the suitability of the topic models for classifying expression microarray data.

Investigating topic models' capabilities in expression microarray data classification.

Grapevine Algerian latent virus (GALV) is a tombusvirus first isolated in 1989 from an Algerian grapevine (Vitis spp.) plant and more recently from water samples and commercial nipplefruit and statice plants. No further reports of natural GALV infections in grapevine have been published in the last two decades, and artificial inoculations of grapevine plants have not been reported. We developed and tested a synthetic GALV construct for the inoculation of Nicotiana benthamiana plants and different grapevine genotypes to investigate the ability of this virus to infect and spread systemically in different hosts.

Construction of a synthetic infectious cDNA clone of Grapevine Algerian latent virus (GALV-Nf) and its biological activity in Nicotiana benthamiana and grapevine plants.

The Arabidopsis Tóxicos en Levadura (ATL) protein family is a class of E3 ubiquitin ligases with a characteristic RING-H2 Zn-finger structure that mediates diverse physiological processes and stress responses in plants. We carried out a genome-wide survey of grapevine (Vitis vinifera L.) ATL genes and retrieved 96 sequences containing the canonical ATL RING-H2 domain. We analysed their genomic organisation, gene structure and evolution, protein domains and phylogenetic relationships. Clustering revealed several clades, as already reported in Arabidopsis thaliana and rice (Oryza sativa), with an expanded subgroup of grapevine-specific genes. Most of the grapevine ATL genes lacked introns and were scattered among the 19 chromosomes, with a high level of duplication retention. Expression profiling revealed that some ATL genes are expressed specifically during early or late development and may participate in the juvenile to mature plant transition, whereas others may play a role in pathogen and/or abiotic stress responses, making them key candidates for further functional analysis. Our data offer the first genome-wide overview and annotation of the grapevine ATL family, and provide a basis for investigating the roles of specific family members in grapevine physiology and stress responses, as well as potential biotechnological applications.

Genome-wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress-responsive and development-related members.

The life cycle of bacterial phytopathogens consists of a benign epiphytic phase, during which the bacteria grow in the soil or on the plant surface, and a virulent endophytic phase involving the penetration of host defenses and the colonization of plant tissues. Innovative strategies are urgently required to integrate copper treatments that control the epiphytic phase with complementary tools that control the virulent endophytic phase, thus reducing the quantity of chemicals applied to economically and ecologically acceptable levels. Such strategies include targeted treatments that weaken bacterial pathogens, particularly those inhibiting early infection steps rather than tackling established infections. This chapter describes a reporter gene-based chemical genomic high-throughput screen for the induction of bacterial virulence by plant molecules. Specifically, we describe a chemical genomic screening method to identify agonist and antagonist molecules for the induction of targeted bacterial virulence genes by plant extracts, focusing on the experimental controls required to avoid false positives and thus ensuring the results are reliable and reproducible.

Application of Chemical Genomics to Plant-Bacteria Communication: A High-Throughput System to Identify Novel Molecules Modulating the Induction of Bacterial Virulence Genes by Plant Signals.

Article	Year
The functions of nitric oxide-mediated signaling and changes in gene expression during the hypersensitive response. Antioxidants & redox signaling\| PubMed ID: 12626115	2003
Improved in planta expression of the human islet autoantigen glutamic acid decarboxylase (GAD65). Transgenic research\| PubMed ID: 12739888	2003
Nitric oxide-mediated transcriptional changes in Arabidopsis thaliana. Molecular plant-microbe interactions : MPMI\| PubMed ID: 14651343	2003
Cross talk between reactive nitrogen and oxygen species during the hypersensitive disease resistance response. Plant physiology\| PubMed ID: 16760491	2006
Expression of Medicago truncatula genes responsive to nitric oxide in pathogenic and symbiotic conditions. Molecular plant-microbe interactions : MPMI\| PubMed ID: 18624641	2008
Investigating topic models' capabilities in expression microarray data classification. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM\| PubMed ID: 23221091	2012
Construction of a synthetic infectious cDNA clone of Grapevine Algerian latent virus (GALV-Nf) and its biological activity in Nicotiana benthamiana and grapevine plants. Virology journal\| PubMed ID: 25367743	2014
Genome-wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress-responsive and development-related members. Scientific reports\| PubMed ID: 27910910	2016
Application of Chemical Genomics to Plant-Bacteria Communication: A High-Throughput System to Identify Novel Molecules Modulating the Induction of Bacterial Virulence Genes by Plant Signals. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 28439871	2017

Annalisa Polverari

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